Dear Carlos,
As my structure has a large and complicated conformational change along two
axes, I am not sure whether TMD is enable of simulating such transition in
a low energy path or just move the structure to lower the RMSD value
regardless of any other parameters.
Both cases (ntr=1. restrantmask) and (ntr=0 and tgtfitmask) worked with a
slight difference. The output shows it recognizes the masks as reported
below:
5. REFERENCE ATOM COORDINATES
defa
Mask :1-114,131-166,188-204,229-249,448-577.CA; matches 318 atoms
Mask ":115-130,167-187,205-228,250-447,578-775.CA" matches 437 atoms
As you mentioned, I used cpptraj to see the changing in the RMSD value. It
decreased until the half and then it increased slowly as it could not find
the final position. The decrease is due to the movement of N-terminal
domain to the reference structure but it should rotate to fit the target.
It seems that the combination of these two movement is not possible at the
same time.
Also, I have tested bigger force constants and the result was not really
desirable as the structure denatured during the movement.
Here are the links to some visualized trajectories:
https://www.dropbox.com/s/weezo4c1hmoc68j/TMD1.mp4?dl=0
https://www.dropbox.com/s/htjdlyuohlglxt5/TMD2.mp4?dl=0
https://www.dropbox.com/s/j7idltd4ax0iaw1/TMD5.mp4?dl=0
On Tue, Nov 27, 2018 at 12:24 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> also your force constant is really small
>
> On Mon, Nov 26, 2018 at 3:52 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > see section 20.4 of the Amber18 manual - you should be using tgtfitmask
> > and tgtrmsmask but I only see tgtrmsmask in your input.
> > I'm not sure what would happen when you also turn on positional
> restraints
> > as you have done here (using ntr=1 and restraintmask)- it might work, but
> > it might not depending on how that matches the other masks. I don't have
> > the ability to check the code right now.
> > what does the beginning of the output say about the targeted md part?
> does
> > it give a fitmask?
> >
> > to check and see if it's working, the best way is to use cpptraj to do
> the
> > rmsd fit to the same reference structure that you gave the md code, using
> > the same mask as you use for tgtfitmask, and then calculate the rmsd next
> > using the tgtrmsmask but including the "nofit" flag. The resulting data
> > stream should match what you asked the md to do (though it's unlikely
> that
> > it can reach exactly 0 rmsd).
> >
> >
> > On Mon, Nov 26, 2018 at 3:22 PM M. Reza Ganjalikhany <
> > ganjalikhany.gmail.com> wrote:
> >
> >> Dear Amber users,
> >>
> >> I am trying to run targeted MD to study a large conformational change
> >> during the simulation between two states of a protein. As I check the
> >> movies from the trajectories, I see that the structure moves from
> initial
> >> to the final structure, but it does not stop at the final point and it
> >> continues to move further beyond the final position. Also, the moving
> part
> >> of the structure hits other parts of the protein and I realize that this
> >> movement will not show the low energy path between the initial and final
> >> conformations.
> >> I have changed the parameters but I couldn't solve the problem. Since I
> >> performed short simulations to see the results quickly, I am not sure
> >> whether I have to set large number for *nstlim *or reduce the *tgtfrc ?
> >> *Is
> >> there any other parameter which is neglected or should be defined in the
> >> input file? The input file has been attached. I wanted to send the
> movies
> >> but it is not possible due to the limitation is the email size.
> >>
> >> I appreciate you valuable comment to tackle this problem.
> >>
> >> Regards,
> >>
> >> Input parameters for targeted MD:
> >> TMD icl2
> >> &cntrl
> >> imin = 0, ntx = 1, nstlim = 12000, irest=0, dt = 0.002, ntc = 2, ntf =
> >> 2,
> >> tol = 0.000001, tempi = 100.0, temp0 = 300.0, cut = 10.0,
> >> ntpr = 10, ntwx = 10, ntwr = 100, ntb = 0, ntt = 1, tautp = 0.5, ntp =
> >> 0,
> >> igb = 1, nscm = 0, nmropt = 1, ntr = 1, restraint_wt=0.02,
> >> itgtmd = 1, tgtrmsd = 39.553, tgtmdfrc = 0.005, restraintmask=
> >> ":1-114,131-166,188-204,229-249,448-577.CA"
> >> tgtrmsmask= ":115-130,167-187,205-228,250-447,578-775.CA",
> >> /
> >> &wt
> >> TYPE='TGTRMSD', istep1=1, istep2=8000,
> >> value1 = 0.0500, value2 = 0.0,
> >> /
> >> &wt
> >> TYPE='TGTRMSD', istep1=8000, istep2=12000,
> >> value1 = 0.0, value2 = 0.0,
> >> /
> >> &wt
> >> type="END",
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> >>
> >
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Received on Thu Nov 29 2018 - 06:00:03 PST
